Hi all,
i want to select only the no of cores to be used instead of both the ppn and node.
Can anyone let me know how can i change the parameters in my job submission script.
Thanks,
ANS
Hi all,
i want to select only the no of cores to be used instead of both the ppn and node.
Can anyone let me know how can i change the parameters in my job submission script.
Thanks,
ANS
The below statement can be used to submit jobs requesting only number of cores, but number of chunks would depend on the default_chunks set at the server level.
qsub -l ncpus=10 – /bin/sleep 10 # this would be scheduled on to a node which has 10 free cores.
The PBS Pro OSS , qsub chunk request system is as below (ppn and nodes are no more used )
qsub -l select=<number_of_chunks>:ncpus=:mem<memory_per_chunk> -l place=
Please check the below section from the https://www.pbsworks.com/pdfs/PBS18.2.3_BigBook.pdf
5.4.8 Platform-specific vs. Generally Available Resources
Hi Adarsh,
Thank you for the reply.
I have used the below script
#!/bin/bash
#PBS -N test
#PBS -S /bin/bash
#PBS -q workq
#$#PBS -l nodes=2:ppn=5
#PBS -l select=1:ncpus=10
#PBS -j oe
cd $PBS_O_WORKDIR
NP=cat $PBS_NODEFILE | wc -l
mpirun -np ${NP} gmx_mpi mdrun -v -s md.tpr
But the job is being executed on single core.
After changing select=2 also still it is running only on 1 core.
Can you help me out.
Thanks,
ANS
ANS,
Please use the below script
#!/bin/bash
#PBS -N test
#PBS -S /bin/bash
#PBS -q workq
#PBS -l select=2:ncpus=5
#PBS -l place=scatter
#PBS -j oe
cd $PBS_O_WORKDIR
NP= `cat PBS_NODEFILE | wc -l\`
mpirun -np {NP} gmx_mpi mdrun -v -s md.tpr
Note:
Thank you
Thank you.
But again we are mentioning the nodes and cpus in different way here.
select=2:ncpus=5 instead of nodes=2:ppn=5
But i require to mention only no of cores, some thing similar to SGE script where we will mention only the no of core.
Thanks,
ANS
Ans,
PBS syntax has been select/ncpus/mem (if i remember correctly since PBS Pro 11.x)
You can submit job as below
qsub -l ncpus=10 -- /bin/sleep
But the number of chunks (select bit) would be used from the server attribute default_chunk.ncpus. So you would be always requesting one chunk.
On the other hand:
qsub -l ncpus=120 -- /bin/sleep 100
qsub -l select=6:ncpus=20 -- /bin/sleep 100
Correction: (Thank you @agurban for this information)
PBS converts old-style resource requests to select and place statements.
See the 18.2 UG, section 4.8.3, "Conversion of Old Style to New", on page UG-70.